strain: FVB;129 treatment: DEN p53 status: WT rb status: KO
Treatment protocol
Fourteen-day-old mice were given a single interperitoneal (i.p.) injection of diethylnitrosamine (DEN) dissolved in 0.9% saline at a dose of 20 mg/kg body weight.
Extracted molecule
total RNA
Extraction protocol
RNA was harvested from frozen liver tissue using RNeasy Blood and Tissue kit (Qiagen, Inc., Valencia, CA) according to the manufacturer's suggested protocols, and quantified on a Nanodrop ND-100 spectrophotometer. RNA quality was assessed by analysis on an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label
biotin
Label protocol
Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)
Hybridization protocol
Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
Scan protocol
Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
Description
15_5-12-10
Data processing
RMA summarization, PM BG correction, and quantile normalization were performed in Affymetrix Expression Console 1.1
